The communication between neurons at synapses occurs in small spaces with small numbers of molecules, far from equilibrium in unmixed volumes. The dynamics of chemical reactions in microdomains is difficult to estimate without having an accurate model of sub-cellular ultrastructure as well as detailed knowledge of the locations and kinetic rate constants of all the relevant molecules, including the neurotransmitter receptors, transporters, binding proteins, degradative enzymes, and other signaling targets. For example, common signaling agents such as calcium have different effects depending on where they enter the cell, and where their targets are located. If the spatial organization of the cell is important, then it is not enough to reconstruct the reaction network of signal transduction pathways. Clearly, to study and understand the behavior of these signaling pathways it is essential to obtain accurate three-dimensional (3-D) anatomical reconstructions of the pathways; that is, to place the signaling pathways within their natural context, which includes the cellular ultrastructure and 3-D distributions of the biochemical molecules. Here, using the MCell Monte Carlo computational modeling program and high-resolution 3-D reconstructions of neural tissue, we propose to explore three components of synaptic signaling: 1) calcium dynamics in the presynaptic boutons from area CA3 pyramidal cells in the rat hippocampus, 2) calcium microdomains in the vicinity of ligand-gated ion channels in postsynaptic calyciform synapses of the avian ciliary ganglion, and 3) extracellular glutamate dynamics in glomeruli from rat cerebellar cortex. These three systems are sufficiently well characterized for quantitative modeling and will allow us to explore the mechanisms underlying the release of neurotransmitter following the entry of calcium into the presynaptic terminal and cross-talk between release sites, the effects of calcium entry into the postsynaptic cell, and the diffusion of neurotransmitter in the synaptic cleft and spillover to neighboring synapses in extracellular space. The detailed level of understanding of these systems afforded by these MCell models will provide new insights that may be applicable to many other synapses, and in particular should help to elucidate how dysfunctions in signaling microdomains may contribute to neurological and psychiatric pathology. PUBLIC HEALTH RELEVANCE: Neurons communicate at synapses, where chemicals released by the presynaptic neuron bind to receptors on the postsynaptic neuron and open channels in the membrane that ions flow through. We will study every aspect of this process using a computer model, called MCell, which simulates every important molecule and chemical interaction between them during synaptic signaling. These studies will help us understand how synapses work and how they dysfunction in neurological and psychiatric pathology.